Sequence
atgc intronic sequence ATGC exonic sequencegtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatca--aacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
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gtaagtga-gataccattct--ccaatattacattctctg------ttcaacatagttgaaatctgcttg--gtaaagttaatttga---ctagtacactttcttaagtataaaatcacaacttgttt-----ccaactcttgctttgcttggctagcaaaccaatctttacg-actctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttcca-tcctcttttccttatattatttatacattaaaat-ttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
| | || | | | | | || | | | | | | | | | ||| | || | || | ||| |||| ||| | || |||||||||||| | ||||| || || || || ||| |||| ||||||| ||| |||||||| || |||||||||||||| ||||| ||||| |||||||
------------------------------------------------------------------------------------------gtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgac-------attattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
| || | | | || | ||| ||| ||| | | | || | | | || ||| | ||| ||||||||||| || | ||||| ||| |||||||| || |||||||| | ||||| |||||||| || || ||||||||||| ||||| ||||| |||||||
------------------------------------------------------------------------------------------------------------gtaacctctagacactcttagtggattggt-ttttaaaaaattgcaatcctaatttatgatttcg----gtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
atcaaacttaaaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG